Aptamer-based colorimetric sensor systems

ABSTRACT

The present invention provides an aptamer-based colorimetric sensor system for determining the presence and optionally the concentration of an analyte in a sample. Methods of utilizing the sensor system and kits that include the sensor also are provided. The sensor utilizes a linker and oligonucleotide functionalized particles to form an aggregate, which disaggregates in response to the analyte.

CROSS REFERENCE TO RELATED APPLICATION

This application is a continuation application of U.S. patent application Ser. No. 11/202,380, filed Aug. 11, 2005, now U.S. Pat. No. 7,892,734 entitled “APTAMER-BASED COLORIMETRIC SENSOR SYSTEMS.”

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This subject matter of this application may have been funded in part under the following research grants and contracts: National Science Foundation Contract Numbers CTS-0120978 and DMR-0117792. The U.S. Government may have rights in this invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May 26, 2011, is named ILL76CON.txt and is 14,947 bytes in size.

BACKGROUND

The ability to determine the presence of an analyte in a sample is of significant benefit. For example, many metals and metal ions, such as lead, mercury, cadmium, chromium, and arsenic, pose significant health risks when present in drinking water supplies. To prevent the contamination of drinking and other water supplies, it is common to test industrial waste-streams before their release to the water treatment plant. Biological fluids, such as blood and those originating from body tissues, also may be tested for a variety of analytes to determine if the body has been exposed to harmful agents or if a disease state exists. For example, the need to detect trace amounts of anthrax in a variety of samples has recently emerged.

Colorimetric methods are commonly used for the detection of metals and ions in soil, water, waste-streams, biological samples, body fluids, and the like. In relation to instrument based methods of analysis, such as atomic absorption spectroscopy, colorimetric methods tend to be rapid and require little in the way of equipment or user sophistication. For example, colorimetric tests are available to aquarists that turn darker shades of pink when added to aqueous samples containing increasing concentrations of the nitrate (NO₃ ⁻) ion. In this manner, colorimetric tests show that the analyte of interest, such as nitrate, is present in the sample and also may provide an indicator of the amount of analyte in the sample through the specific hue of color generated. While conventional colorimetric tests are extremely useful, they only exist for a limited set of analytes, and often cannot detect very small or trace amounts of the analyte.

As can be seen from the above description, there is an ongoing need for colorimetric sensor systems that can identify trace amounts of a broader scope of analytes and that increase the reliability of the analysis.

SUMMARY

A sensor system for detecting an analyte includes a linker comprising an aptamer that folds in response to the analyte and second particles coupled to a second oligonucleotide that is complementary to at least a portion of the aptamer. The linker may include an extension where a first oligonucleotide coupled to first particles is complementary to at least a portion of the extension.

A method of detecting an analyte includes combining an aggregate with a sample to detect a color change responsive to the analyte. The aggregate may include a linker and second particles. The aggregate also may include first particles and the linker may include an extension.

A kit for detecting an analyte includes a first container containing a system for forming aggregates that includes second particles and a linker including an aptamer, which folds in response to the analyte. The second particles are coupled to second oligonucleotides that are complementary to at least a portion of the aptamer.

A method for determining the sensitivity and selectivity of an aptamer to an analyte includes combining an aggregate with the analyte, detecting a color change responsive to the analyte, and determining if the DNA strand folded to provide the color change. The aggregate includes second particles and a linker including a DNA strand. The aggregate also may include first particles. The linker may include an extension.

In order to provide a clear and consistent understanding of the specification and claims, the following definitions are provided.

The term “sample” is defined as a composition that will be subjected to analysis that is suspected of containing the analyte of interest. Typically, a sample for analysis is in a liquid form, and preferably the sample is an aqueous mixture. A sample may be from any source, such as an industrial sample from a waste-stream or a biological sample, such as blood, urine, or saliva. A sample may be a derivative of an industrial or biological sample, such as an extract, a dilution, a filtrate, or a reconstituted precipitate.

The term “analyte” is defined as one or more substance potentially present in the sample. The analysis determines the presence, quantity, or concentration of the analyte present in the sample.

The term “colorimetric” is defined as an analysis where the reagent or reagents constituting the sensor system produce a color change in the presence or absence of an analyte.

The term “light-up” refers to a colorimetric sensor system that undergoes a desired color change in response to an analyte present in a sample.

The term “light-down” refers to a colorimetric sensor system that does not undergo a color change when an analyte is present in a sample, but does undergo a desired color change in the absence of the analyte.

The term “sensitivity” refers to the smallest increase in an analyte concentration that is detectable by the sensor system (resolution) or to the lowest concentration limit at which a sensor system can differentiate a signal responsive to the analyte from a background signal (detection limit). Thus, the more sensitive a sensor system is to an analyte, the better the system is at detecting lower concentrations of the analyte.

The term “selectivity” refers to the ability of the sensor system to detect a desired analyte in the presence of other species.

The term “hybridization” refers to the ability of a first polynucleotide to form at least one hydrogen bond with at least one second nucleotide under low stringency conditions.

The term “aptamer” refers to a strand of nucleic acids that undergoes a conformational change in response to an analyte.

The term “conformational change” refers to the process by which an aptamer adopts a tertiary structure from another state. For simplicity, the term “fold” may be substituted for conformational change.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention can be better understood with reference to the following drawings and description. The components in the figures are not necessarily to scale and are not intended to accurately represent molecules or their interactions, emphasis instead being placed upon illustrating the principles of the invention.

FIG. 1 represents a colorimetric analysis for determining the presence and optionally the concentration of an analyte in a sample.

FIG. 2A depicts an aptamer that depends on two analyte molecules to fold.

FIG. 2B depicts the base pairs for an aptamer depending on two adenosine molecules to fold (SEQ ID NO: 57).

FIG. 2C depicts an aptamer joined to an extension to form a linker.

FIG. 3A represents the disaggregation of an aggregate in the presence of an adenosine analyte (SEQ ID NOS: 46, 45, 44).

FIG. 3B represents the tail-to-tail hybridization of oligonucleotide functionalized particles with a linker.

FIG. 3C represents the head-to-tail hybridization of oligonucleotide functionalized particles with a linker.

FIG. 3D represents the head-to-head hybridization of oligonucleotide functionalized particles with a linker.

FIG. 4 is a graph relating extinction ratios to the wavelengths of light emitted from a sample by aggregated (solid line) and disaggregated (dashed line) gold nanoparticles.

FIG. 5A is a graph showing the change in extinction ratios over time for samples containing guanosine (◯), cytidine (▴), uridine (□), and adenosine (●).

FIG. 5B is a graph depicting the correlation between the observed extinction ratios for the color change of the sensor system and the concentration of the adenosine analyte after one minute.

FIG. 5C is a graph depicting the extinction ratios for multiple adenosine concentrations over a 6 minute time period.

FIG. 6A provides the sequences of the extension and aptamer portions of a linker and of the oligonucleotide functionalized particles for a potassium ion sensor system (SEQ ID NOS: 52, 53, and 44, respectively in order of appearance).

FIG. 6B depicts the aptamer folding in the presence of the K(I) analyte (SEQ ID NO: 1).

FIG. 6C depicts the extinction ratio of the potassium ion sensor for multiple metal ions.

FIG. 7A provides the sequences of the extension and aptamer portions of a linker and of the oligonucleotide functionalized particles for a cocaine sensor system (SEQ ID NOS: 54, 58 and 44, respectively in order of appearance).

FIG. 7B depicts the aptamer folding in the presence of the cocaine analyte (SEQ ID NO: 59).

FIG. 8A is a graph showing the change in extinction ratios over time for samples containing adenosine (Δ), sucrose (◯), and cocaine (●).

FIG. 8B is a graph depicting the correlation between the observed extinction ratios for the color change of the sensor system and the concentration of the cocaine analyte after 1 minute of aggregation.

FIG. 8C is a graph depicting the extinction ratios for multiple cocaine analyte concentrations over a 5 minute time period.

DETAILED DESCRIPTION

Aptamers may be easier to isolate than nucleic acid based catalysts. The simpler structure of aptamers in relation to nucleic acid enzymes also may allow for the design of analyte sensor systems for which nucleic acid enzymes are not available. The present invention makes use of the discovery that by selecting the hybridization strength between the folded and unfolded conformations of an aptamer and an oligonucleotide functionalized particle, the particle may be released in response to an analyte. In this manner, a light-up colorimetric sensor is provided that undergoes a desired color change in response to a selected analyte at room temperature, thus overcoming a disadvantage of the sensor system disclosed in U.S. Ser. No. 10/144,679.

FIG. 1 represents a colorimetric analysis 100 for determining the presence and optionally the concentration of an analyte 105 in a sample 102. In 110, the analyte 105 for which the method 100 will determine the presence/concentration of is selected.

In one aspect, the analyte 105 may be any ion that causes an aptamer 124 to fold. In another aspect, the analyte 105 may be any metal ion that causes an aptamer 124 to fold. Preferable monovalent ions having a ⁺1 formal oxidation state (I) include NH₄ ⁺, K(I), Li(I), Tl(I), and Ag(I). Preferable divalent metal ions having a ⁺2 formal oxidation state (II) include Mg(II), Ca(II), Mn(II), Co(II), Ni(II), Zn(II), Cd(II), Cu(II), Pb(II), Hg(II), Pt(II), Ra(II), Sr(II), Ni(II), and Ba(II). Preferable trivalent and higher metal ions having ⁺3 (III), ⁺4 (IV), ⁺5 (V), or ⁺6 (VI) formal oxidation states include Co(III), Cr(III), Ce(IV), As(V), U(VI), Cr(VI), and lanthanide ions. More preferred analyte ions include monovalent metal ions and metal ions that are toxic to living organisms, such as Ag(I), Pb(II), Hg(II), U(VI), and Cr(VI).

In another aspect, the analyte 105 may be any biomolecule that causes the aptamer 124 to fold. Preferable biomolecules include large biomolecules, such as proteins (e.g. proteins related to HIV, hCG-hormone, insulin), antibodies, growth factors, enzymes, virus (e.g. HIV, small pox), viral derived components (e.g. HIV-derived molecules), bacteria (e.g. anthrax), bacteria derived molecules and components (e.g. anthrax derived molecules), or cells. Preferable biomolecules also may include small biomolecules, such as amino acids (e.g. arginine), nucleotides (e.g. ATP, GTP), neurotransmitters (e.g. dopamine), cofactors (e.g. biotin), peptides, or amino-glycosides.

In another aspect, the analyte 105 may be any organic molecule that causes the aptamer 124 to fold. Preferable organic molecules include drugs, such as antibiotics and theophylline, or controlled substances, such as cocaine, dyes, oligosaccharides, polysaccharides, glucose, nitrogen fertilizers, pesticides, dioxins, phenols, 2,4-dichlorophenoxyacetic acid, nerve gases, trinitrotoluene (TNT), or dinitrotoluene (DNT).

Once the analyte 105 is selected, the one or more aptamer 124 is selected that folds in response to the analyte 105. The aptamer selection 120 may be performed by in vitro selection, directed evolution, or other method known to those of ordinary skill in the art. The aptamer selection 120 may provide one or more aptamers that demonstrate enhanced folding in the presence of the selected analyte 105 (thereby providing sensor sensitivity). The selection 120 also may exclude aptamers that fold in the presence of selected analytes, but that do not fold in the presence of non-selected analytes and/or other species present in the sample 102 (thereby providing sensor selectivity).

For example, an aptamer may be selected that specifically binds K(I), while not significantly binding Na(I), Li(I), Cs(I), Rb(I), or other competing metal ions. In one aspect, this may be achieved by isolating aptamers that bind K(I), then removing any aptamers that bind Na(I), Li(I), Cs(I), or Rb(I). In another aspect, aptamers that bind Na(I), Li(I), Cs(I), or Rb(I) are first discarded and then those that bind K(I) are isolated. In this manner, the selectivity of the aptamer may be increased.

The aptamer 124 includes a nucleic acid strand that folds in the presence of the analyte 105. In one aspect, the folding may be considered the conversion of a primary or duplex structure to a tertiary structure. The base sequence of the aptamer may be designed so that the aptamer may undergo at least partial hybridization with at least one oligonucleotide functionalized particle. In this aspect, at least a portion of the base sequence of the aptamer 124 may be complementary to at least one oligonucleotide of the oligonucleotide functionalized particle.

The aptamer 124 may be formed from deoxyribonucleotides, which may be natural, unnatural, or modified nucleic acids. Peptide nucleic acids (PNAs), which include a polyamide backbone and nucleoside bases (available from Biosearch, Inc., Bedford, Mass., for example), also may be useful.

Table I below lists analytes, the aptamer or aptamers that bind with and fold in response to that analyte, and the reference or references where the sequence of each aptamer is described. The analyte binding region of these, and other, aptamers may be adapted for use in a linker 128. For example, the non-analyte binding region of the cocaine aptamer, given as SEQ ID NO: 10 in Table I below, may be modified to provide the aptamer GGGAGACAAGGATAAATCCTTCAATGAAGTGGGTCTCCC (SEQ ID NO: 56) and included in the linker 128.

TABLE I Analyte class Example Aptamer Motif Sequence (SEQ ID NO:) Ref Metal ions K(I) GGGTTAGGGTTAGGGTTAGGG 1 (SEQ ID NO: 1) Zn(II) AGGCGAGGUGAAAUGAGCGGUAAUAGCCU 2 (SEQ ID NO: 2) Ni(II) GGGAGAGGAUACUACACGUGAUAGUCAGGGAAC 3 AUGACAAACACAGGGACUUGCGAAAAUCAGUGU UUUGCCAUUGCAUGUAGCAG AAGCUUCCG (SEQ ID NO: 3) Organic Cibacron GGGAGAATTCCCGCGGCAGAAGCCCACCTGGCT 4 dyes blue TTGAACTCTATGTTATTGGGTGGGGGAAACTTA AGAAAACTACCACCCTTCAACATTACCGCCCTT CAGCCTGCCAGCGCCCTGCAGCCCGGGAAGCTT (SEQ ID NO: 4) Malachite GGAUCCCGACUGGCGAGAGCCAGGUA ACGAAU 5 green GGAUCC (SEQ ID NO: 5) Sulforhodamine CCGGCCAAGGGTGGGAGGGAGGGGGCCGG 6 B (SEQ ID NO: 6) Small Biotin AUGGCACCGACCAUAGGCUCGGGUUGCCAGAGG 7 organic UUCCACACUUUCAUCGAAAAGCCUAUGC molecules (SEQ ID NO: 7) Theophylline GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGUC 8 (SEQ ID NO: 8) Adenine GAUAGGACGAUUAUCGAAAAUCACCAGAUUGGA 9 CCCUGGUUAACGAUCCAUU (SEQ ID NO: 9) Cocaine GGGAGACAAGGATAAATCCTTCAATGAAGTGGG 10 TCGACA (SEQ ID NO: 10) Dopamine GGGAAUUCCGCGUGUGCGCCGCGGAAGAGGGAA 11 UAUAGAGGCCAGCACAUAGUGAGGCCCUCCUCC C (SEQ ID NO: 11) Amino acids Arginine GGGAGCUCAGAAUAAACGCUCAAGGAGGACCGU 12 GCACUCCUCGAACAUUUCGAGAUGAGACACGGA UCCUGC (SEQ ID NO: 12) Citrulline GACGAGAAGGAGUGCUGGUUAUACUAGCGGUUA 13 GGUCACUCGUC (SEQ ID NO: 13) Nucleosides & ATP ACCTGGGGGAGTATTGCGGAGGAAGGT 14 nucleotides (SEQ ID NO: 14) cAMP GGAAGAGAUGGCGACUAAAACGACUUGUCGC 15 (SEQ ID NO: 15) GTP UCUAGCAGUUCAGGUAACCACGUAAGAUACGGG 16 UCUAGA (SEQ ID NO: 16) Guanosine GGGAGCUCAGAAUAAACGCUCAACCCGACAGAU 17 CGGCAACGCCNUGUUUUCGACANGAGACACCGA UCCUGCACCAAAGCUUCC (SEQ ID NO: 17) Adenosine ACCTGGGGGAGTATTGCGGAGGAAGGT 18 (SEQ ID NO: 18) RNA TAR-RNA GCAGTCTCGTCGACACCCAGCAGCGCATGTAAC 19 TCCCATACATGTGTGTGCTGGATCCGACGCAG (SEQ ID NO: 19) Biological CoA GGGCACGAGCGAAGGGCAUAAGCUGACGAAAGU 20 cofactors CAGACAAGACAUGGUGCCC (SEQ ID NO: 20) NMN GGAACCCAACUAGGCGUUUGAGGGGAUUCGGCC 21 ACGGUAACAACCCCUC (SEQ ID NO: 21) FAD GGGCAUAAGGUAUUUAAUUCCAUACAAGUUUAC 22 AAGAAAGAUGCA (SEQ ID NO: 22) Porphyrin TAAACTAAATGTGGAGGGTGGGACGGGAAGAAG 23 TTTA (SEQ ID NO: 23) Vitamin B12 CCGGUGCGCAUAACCACCUCAGUGCGAGCAA 24 (SEQ ID NO: 24) Amino- Tobramycin GGGAGAAUUCCGACCAGAAGCUUUGGUUGUCUU 25 glycosides GUACGUUCACUGUUACGAUUGUGUUAGGUUUAA CUACACUUUGCAAUCGCAUAUGUGCGUCUACAU GGAUCCUCA (SEQ ID NO: 25) Oligo- Cellobiose GCGGGGTTGGGCGGGTGGGTTCGCTGGGCAGGG 26 saccharides GGCGAGTG (SEQ ID NO: 26) Poly- Sephadex UACAGAAUGGGUUGGUAGGCAUACCUAAUCGAG 27 saccharides AAUGAUA (SEQ ID NO: 27) Antibiotics Viomycin GGAGCUCAGCCUUCACUGCAAUGGGCCGCUAGG 28 UUGAUGUGCAGUGAAGUCAGCUGAGGCCCAGGG CUGAAAGGAUCGCCCUCCUCGACUCGUGGCACC ACGGUCGGAUCCAC (SEQ ID NO: 28) Streptomycin GGAUCGCAUUUGGACUUCUGCCCAGGGGGCACC 29 ACGGUCGGAUCC (SEQ ID NO: 29) Tetracycline GGCCUAAAACAUACCAGAUUUCGAUCUGGAGAG 30 GUGAAGAAUUCGACCACCUAGGCCGGU (SEQ ID NO: 30) Vasopressin ACGTGAATGATAGACGTATGTCGAGTTGCTGTG 31 TGCGGATGAACGT (SEQ ID NO: 31) Peptides Substance P GGGAGCUGAGAAUAAACGCUCAAGGGCAACGCG 32 GGCACCCCGACAGGUGCAAAAACGCACCGACGC CCGGCCGAAGAAGGGGAUUCGACAUGAGGCCCG GAUCCGGC (SEQ ID NO: 32) Enzymes HIV UCCGUUUUCAGUCGGGAAAAACUG 33 Rev (SEQ ID NO: 33) Transscriptase Human thrombin GGTTGGTGTGGTTGG 34 (SEQ ID NO: 34) Growth VEGF₁₆₅ GCGGUAGGAAGAAUUGGAAGCGC 35 factors (SEQ ID NO: 35) Transcription NF-KB GGGAUAUCCUCGAGACAUAAGAAACAAGAUAGA 36 factors UCCUGAAACUGUUUUAAGGUUGGCCGAUCUUCU GCUCGAGAAUGCAUGAAGCGUUCCAUAUUUUU (SEQ ID NO: 36) Antibodies Human IgE GGGGCACGTTTATCCGTCCCTCCTAGTGGCGTG 37 CCCC (SEQ ID NO: 37) Gene Elongation GGGGCUAUUGUGACUCAGCGGUUCGACCCCGCU 38 Regulatory factor Tu UAGCUCCACCA factors (SEQ ID NO: 38) Cell Human CD4 UGACGUCCUUAGAAUUGCGCAUUCCUCAC 39 adhesion ACAGGAUCUU molecules (SEQ ID NO: 39) cells YPEN-1 ATACCAGCTTATTCAATTAGGCGGTGCATTGTG 40 endothelial GTTGGTAGTATACATGAGGTTTGGTTGAGACTA GTCGCAAGATATAGATAGTAAGTGCAATCT (SEQ ID NO: 40) Viral/bacterial Anthrax spores Sequences are not given 41 components Rous AGGACCCUCGAGGGAGGUUGCGCAGGGU 42 sarcoma virus (SEQ ID NO: 42)

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After selecting an appropriate aptamer or aptamers in 120, a linker 128 is formed that includes the aptamer 124. In one aspect, the aptamer 124 may serve directly as the linker 128. In another aspect, the linker 128 may be formed by joining the aptamer 124 with one or more extensions 126.

The extension 126 may be any nucleic acid sequence that may be joined with the aptamer 124, that may undergo at least partial hybridization with one or more oligonucleotide functionalized particles, and that is compatible with the analysis 100. In this aspect, at least a portion of the base sequence of the extension 126 may be complementary to at least one oligonucleotide of one or more oligonucleotide functionalized particle. In one aspect, solid phase synthesis may be used to join the aptamer 124 with the extension 126 to form the linker 128. In another aspect, after the aptamer 124 portion of the linker 128 is synthesized, the synthesis is continued to form the extension 126. Similarly, the linker 128 may be extended with the aptamer 124 sequence.

Preferably, the extension 126 includes from 1 to 100 bases. In one aspect, at least 50, 70, or 90% of the bases present in the extension 126 are capable of hybridizing with a complementary portion of a first oligonucleotide functionalized particle, such as the TGAGTAGACACT-5′ (SEQ ID NO: 43) portion of particle 336 in FIG. 3A, while at least 50, 35, 25, or 10% of the bases present in the extension are capable of hybridizing with a second oligonucleotide functionalized particle, such as particle 337 in FIG. 3A.

After selecting or synthesizing the linker 128, an aggregate 132 may be formed in 130. The aggregate 132 includes the linker 128 and oligonucleotide functionalized particles 136. Considering the physical size of its components, the aggregate 132 may be quite large.

The linker 128 hybridizes with the oligonucleotide functionalized particles 136 and includes the aptamer 124 and may include the extension 126. For example, if first and second oligonucleotide functionalized particles have base sequences of 3′-AAAAAAAAAAAATGAGTAGACACT (SEQ ID NO: 44) and 5′-CCCAGGTTCTCT (SEQ ID NO. 45), respectively, an appropriate sequence for the linker 128 that includes the aptamer 124 that folds in the presence of an adenosine analyte and the extension 126 may be 5′-ACTCATCTGTGAAGAGAACCTGGGGGAGTATTGCGGAGGAAGGT (SEQ ID NO. 46).

For the adenosine analyte, the extension 126 portion of the linker 128 is the ACTCATCTGTGAAGAGA (SEQ ID NO: 47) portion of the sequence, which allows the extension 126 to hybridize with twelve bases of the first functionalized particle and five bases of the second functionalized particle. Similarly, the aptamer 124 portion of the linker 128 is the ACCTGGGGGAGTATTGCGGAGGAAGGT (SEQ ID NO: 18) portion of the sequence, which allows the ACCTGGG (SEQ ID NO: 48) portion of the aptamer 124 to hybridize with the TGGACCC (SEQ ID NO: 49) portion of the second functionalized particle.

Because the particles 136 demonstrate distance-dependent optical properties, the particles are one color when closely held in the aggregate 132 and undergo a color change as the distance between the particles increases. For example, when the particles 136 are gold nanoparticles, the aggregate 132 displays a blue color in aqueous solution that turns red as disaggregation proceeds.

Disaggregation occurs when the aptamer 124 portion of the linker 128 binds with and folds in response to the analyte 105. When the aptamer 124 folds, a portion of the hybridization with the second oligonucleotide functionalized particles is lost. This hybridization loss allows the second oligonucleotide functionalized particles to separate from the aggregate 132. Thus, as the particles 136 diffuse away from the aggregate 132, the solution changes from blue to red.

The particles 136 may be any species that demonstrate distance-dependent optical properties and are compatible with the operation of the sensor system. Suitable particles may include metals, such as gold, silver, copper, and platinum; semiconductors, such as CdSe, CdS, and CdS or CdSe coated with ZnS; and magnetic colloidal materials, such as those described in Josephson, Lee, et al., Angewandte Chemie, International Edition (2001), 40(17), 3204-3206. Specific useful particles may include ZnS, ZnO, TiO₂, AgI, AgBr, HgI₂, PbS, PbSe, ZnTe, CdTe, In₂S₃, In₂Se₃, Cd₃P₂, Cd₃As₂, InAs, and GaAs.

In a preferred aspect, the particles are gold (Au) nanoparticles and have an average diameter from 5 to 70 nanometers (nm) or from 10 to 50 nm. In a more preferred aspect, gold nanoparticles having an average diameter of from 10 to 15 nm are functionalized to the oligonucleotides.

For a more detailed treatment of how to prepare oligonucleotide functionalized gold particles, See U.S. Pat. No. 6,361,944; Mirkin, et al., Nature (London) 1996, 382, 607-609; Storhoff, et al., J. Am. Chem. Soc. 1998, 20, 1959-1064; and Storhoff, et al., Chem. Rev. (Washington, D.C.) 1999, 99, 1849-1862. While gold nanoparticles are presently preferred, other species that undergo a distance-dependent color change, such as inorganic crystals, quantum dots, and the like also may be attached to oligonucleotides.

In 140 the aggregate 132 may be combined with the sample 102. In 150 the sample 102 is monitored for a color change. If a color change does not occur, then the analyte 105 is not present in the sample 102. If a color change does occur in 160, the analyte 105 is present in the sample 102. The color change signifies that the analyte 105 caused the aptamer 124 to fold, thus allowing the particles 136 to diffuse away from the aggregate 132 and into the solution of the sample 102. Thus, the analysis 100 provides a “light-up” sensor system because a color change occurs in the presence of the analyte 105.

The rate at which a substantially complete color change occurs in response to the analyte 105 may be considered the response time of the sensor system. In one aspect, the color change may be considered substantially complete when the absorption peak in the visible region increases by 20%. In another aspect, the color change may be considered substantially complete when the extinction coefficient at 522 nm over 700 nm increases by 100% for gold particles. Preferable response times for the sensor system are from 1 second to 60 minutes or from 2 seconds to 10 minutes. More preferable response times for the sensor system are from 5 seconds to 2 minutes or from 8 to 12 seconds. Preferable temperature ranges for operation of the sensor system are from 0° to 60° or from 15° to 40° C. More preferable ranges for operation of the sensor system are from 23° to 37° or from 25° to 30° C. In another aspect, when the analysis 100 is conducted from 23° to 37° C., a preferable response time may be less than 2 minutes or from 1 to 12 seconds.

The degree the color changes in response to the analyte 105 may be quantified by colorimetric quantification methods known to those of ordinary skill in the art in 170. Various color comparator wheels, such as those available from Hach Co., Loveland, Colo. or LaMotte Co., Chestertown, Md. may be adapted for use with the present invention. Standards containing known amounts of the selected analyte may be analyzed in addition to the sample to increase the accuracy of the comparison. If higher precision is desired, various types of spectrophotometers may be used to plot a Beer's curve in the desired concentration range. The color of the sample may then be compared with the curve and the concentration of the analyte present in the sample determined. Suitable spectrophotometers include the Hewlett-Packard 8453 and the Bausch & Lomb Spec-20.

In yet another aspect, the method 100 may be modified to determine the sensitivity and selectivity of an aptamer to the analyte 105. In this aspect, one or more DNA strand suspected of being an aptamer responsive to the analyte 105 is selected in 120. The DNA strand may or may not be modified with the extension 126 in 125. In 130, an aggregate is formed from the DNA strands and appropriate particles. In 140, the aggregates are combined with the analyte 105. If the aggregate undergoes a color change, then the DNA strand is an appropriate aptamer sequence for the target 105. In this manner, multiple aptamers selected in 120 may be tested for use in a colorimetric sensor system.

FIG. 2A depicts an aptamer 224 that depends on two analyte molecules to undergo a conformational change to adopt a folded structure 230. FIG. 2B depicts the specific base pairs of the aptamer 224 that forms the folded structure 230 in response to two adenosine molecules. While this specific aptamer sequence relies on two molecules of the adenosine analyte to fold, other aptamers may fold in response to a single analyte molecule.

FIG. 2C depicts the aptamer 224 joined to an extension 226 to form a linker 228. The extension 226 includes A and B portions, where the A portion includes enough complementary bases to form stable hybridization with the oligonucleotide of a first particle 236. For example, a non-complementary poly-adenine chain (A₁₂) including 12 adenine bases may be appended to the complementary sequence of the first particle 236 to enhance hybridization stability. The sequence for the B portion of the extension 226 may be selected to eliminate linkers that inherently form stable secondary structures. A computer program, such as M-fold available at (www.bioinfospi.edu/applications/mfold/) (M. Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-15, (2003)) or others, may be used to predict stable linkers for elimination. For example if a stable sequence for a linker is ACTCATCTGTGAAGA TGACCTGGGGGAGTATTGCGGAGGAAGGT (SEQ ID NO: 50), by substituting the underlined TG bases for GA bases to give the sequence ACTCATCTGTGAAGA GAACCTGGGGGAGTATTGCGGAGGAAGGT (SEQ ID NO: 51), the linker may be rendered inherently unstable.

The aptamer 224 includes C and D portions. In one aspect, the hybridization stability of the combined B portion of the extension 226 and the C portion of the aptamer 224 with the second particle 237 may be less than that for A and the first particle 236. In a preferred aspect, the melting temperature of this C+B/second particle hybridization is higher than the temperature at which the sensor system is to be used. In another preferred aspect, the melting temperature of a B portion hybridized to the oligonucleotide sequence of the second particle 237 is less than the temperature at which the sensor system is to be used. In another preferred aspect, the stability of a C+D+analyte complex should be greater than the hybridization stability of C with the second particle 237. In another aspect, the sequences of B and C are as short as is compatible with the operation of the sensor system.

FIG. 3A depicts the disaggregation of an aggregate 332 in the presence of an adenosine analyte 305. The aggregate 332 is formed from multiple aggregate units 331. Each of the aggregate units 331 is formed from a linker 328, which is hybridized to the 3′ and 5′ thiol-oligonucleotide functionalized particles 336 and 337, respectively. The linker 328 includes an aptamer portion 324 and an extension portion 326. The 3′-A₁₂Ade_(Au) (SEQ ID NO: 44) particle 336 hybridizes with the extension 326, while the 5′-Ade_(Au) particle 337 hybridizes with the extension 326 and the aptamer 324 to from the aggregate unit 331.

While one base sequence for the linker and the particles are shown, the bases may be changed on the opposing strands to maintain the pairings. For example, any cytosine in the A or B portions of the linker 228 may be changed to thymine, as long as the paired base of the particle oligonucleotide is changed from guanine to adenine.

In the presence of the adenosine analyte 305, the aptamer portion 324 of the linker 328 folds, thus eliminating at least a portion of the hybridization between the aptamer portion 324 of the linker 328 and the 5′-Ade_(Au) particle 337. This loss of hybridization between the aptamer 324 and the 5′-Ade_(Au) particle 337 releases the 5′-Ade_(Au) particle to the solution.

As the 5′-Ade_(Au) particles 337 are released, the blue aggregate 332 begins to disaggregate to form partial aggregate 390. This partial disaggregation adds red color to the blue solution as the particles 337 diffuse away from the aggregate 332, thus giving a purple solution. If enough of the adenosine analyte 305 is present in the sample, the reaction will continue until the aggregate 332 is completely disaggregated, to give 395. Complete disaggregation results in a red solution due to the greater distance between the particles 336, 337.

The alignment of the particles 336, 337 (tail-to-tail, head-to-tail, or head-to-head) with respect to each other may influence how tightly the aggregate units 331 bind. FIG. 3B depicts the aggregate unit 331 formed when the functionalized particles, such as 336 and 337, hybridize to the linker 328 in a tail-to-tail arrangement. Head-to-tail (FIG. 3C) or head-to-head (FIG. 3D) hybridization may be selected by reversing one or both ends of the oligonucleotide to which the particle is attached, respectively. Thus, by reversing the 3′ attachment of functionalized particle 336 to 5′, particle 338 may hybridize to give the head-to-tail alignment of FIG. 3C. Similarly by reversing the 3′ attachment of the functionalized particle 336 to the 5′ attachment of the particle 338 and by reversing the 5′ attachment of the particle 337 to the 3′ attachment of particle 339, the particles 338, 339 may hybridize to give the head-to-head alignment of FIG. 3D.

At present, the tail-to-tail hybridization arrangement of FIG. 3B is preferred because the head-to-tail and head-to-head hybridization arrangements of FIGS. 3C and 3D may produce aggregates that sterically hinder aptamer binding and/or aggregate formation. However, this steric hindrance may be reduced through a reduction in the average diameter of the particles or by increasing the number of bases functionalized to the particles and the length of the extension, for example.

While not shown, the methodology of FIG. 3A may be applied to other analytes, including potassium ions, cocaine, and the analytes listed above in Table I. Table II, below, gives the base sequences of the linkers and particles for adenosine, K(I), and cocaine sensor systems. The aptamer portion of each linker is presented in uppercase, while the extension portion of each linker is presented in lowercase.

TABLE II SEQ Name Sequence ID NO: Adenosine 5′-actcatctgtgaagagaACCTGGGGGAG 46 Linker TATTGCGGAGGAAGGT 3′-A₁₂Ade_(Au) 3′-AAAAAAAAAAAATGAGTAGACACT 44 5′-Ade_(Au) 5′-CCCAGGTTCTCT 45 Potassium 5′-actcatctgtgatctaaGGGTTAGGGTT 52 Linker AGGGTTAGGG 3′-A₁₂K(I)_(Au) 3′-AAAAAAAAAAAATGAGTAGACACT 44 5′-K(I)_(Au) 5′-AACCCTTAGA 53 Cocaine 5′-actcatctgtgaatctcGGGAGACAAGG 54 Linker ATAAATCCTTCAATGAAGTGGGTCTCCC 3′- A₁₂Coc_(Au) 3′-AAAAAAAAAAAATGAGTAGACACT 44 5′-Coc_(Au) 5′-GTCTCCCGAGA 55

The ionic strength of the sample may influence how tightly the moieties that form the aggregate bind together. Higher salt concentrations favor aggregation, thus slowing sensor response, while lower salt concentrations may lack the ionic strength necessary to maintain the aggregates. In one aspect, the sample may include or be modified with a reagent to include a monovalent metal ion concentration of 30 mM and greater. The ionic strength of the sample may be modified with Na⁺ ions, for example. In a preferred aspect, the monovalent metal ion concentration of the sample, which contains the aggregate, is from 150 to 400 mM. At present, especially preferred monovalent metal ion concentrations are about 300 mM for adenosine and potassium analytes and about 150 mM for cocaine as an analyte. pH also may influence the aggregate binding, possibly attributable to the protonation of the polynucleotide base pairs at lower pH. In one aspect, a pH from 5 to 9 is preferred, with an approximately neutral pH being more preferred.

Thus, the performance of the sensor may be improved by adjusting the ionic strength and pH of the sample prior to combining it with the aggregate. Depending on the sample, it may be preferable to add the sample or analyte to a solution containing the aggregate (where the ionic strength and pH may be controlled) or the reverse.

The sensor system, including the aptamer, extension, and oligonucleotide functionalized particles may be provided in the form of a kit. In one aspect, the kit includes the aptamer and the extension joined to form the linker. In yet another aspect, the kit includes the extension, but excludes the aptamer, which is then provided by the user or provided separately. In this aspect, the kit also may include the reagents required to link the supplied extension with an aptamer. In this aspect, the kit also may be used to determine the specificity and/or selectivity of various aptamers to a selected analyte. Thus, the kit may be used to select an appropriate aptamer in addition to detecting the analyte. In yet another aspect, the kit includes an exterior package that encloses a linker and oligonucleotide functionalized particles.

One or more of these kit components may be separated into individual containers, or they may be provided in their aggregated state. If separated, the aggregate may be formed before introducing the sample. Additional buffers and/or pH modifiers may be provided in the kit to adjust the ionic strength and/or pH of the sample.

The containers may take the form of bottles, tubs, sachets, envelopes, tubes, ampoules, and the like, which may be formed in part or in whole from plastic, glass, paper, foil, MYLAR®, wax, and the like. The containers may be equipped with fully or partially detachable lids that may initially be part of the containers or may be affixed to the containers by mechanical, adhesive, or other means. The containers also may be equipped with stoppers, allowing access to the contents by syringe needle. In one aspect, the exterior package may be made of paper or plastic, while the containers are glass ampoules.

The exterior package may include instructions regarding the use of the components. Color comparators; standard analyte solutions, such as a 10 μm solution of the analyte; and visualization aids, such as thin layer chromatography (TLC) plates, test tubes, and cuvettes, also may be included. Containers having two or more compartments separated by a membrane that may be removed to allow mixing may be included. The exterior package also may include filters and dilution reagents that allow preparation of the sample for analysis.

In another aspect, in addition to the sensor system of the present invention, the kit also may include multiple sensor systems to further increase the reliability of analyte determination and reduce the probability of user error. In one aspect, multiple light-up sensor systems in accord with the present invention may be included. In another aspect, a “light-down” sensor system may be included with the light-up sensor system of the present invention. Suitable light-down sensors for inclusion in the presently claimed kit may rely on DNAzyme/Substrate/particle aggregates that are not formed in the presence of the selected analyte. A more detailed description of suitable light-down sensor systems for inclusion in the presently claimed kit may be found, for example, in U.S. patent application Ser. No. 10/756,825, filed Jan. 13, 2004, entitled “Biosensors Based on Directed Assembly of Particles,” which is hereby incorporated by reference.

The preceding description is not intended to limit the scope of the invention to the described embodiments, but rather to enable a person of ordinary skill in the art to make and use the invention. Similarly, the examples below are not to be construed as limiting the scope of the appended claims or their equivalents, and are provided solely for illustration. It is to be understood that numerous variations can be made to the procedures below, which lie within the scope of the appended claims and their equivalents.

EXAMPLES

All DNA samples were purchased from Integrated DNA Technology Inc., Coralville, Iowa. The DNA samples that formed the extensions were purified by gel electrophoresis, while the thiol-modified DNA samples for forming the oligonucleotide functionalized particles were purified by standard desalting. Adenosine, cytidine, uridine, guanosine and cocaine were purchased from Aldrich. Gold nanoparticles having an average diameter of 13 nm were prepared and functionalized with 12-mer thiol-modified DNA following literature procedures, such as those disclosed in Storhoff, J., et al., “One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold particle probes,” JACS 120: 1959-1964 (1998), for example. The average diameter of the gold nanoparticles was verified by transmission electronic microscope (JEOL 2010).

Example 1 Preparation of a Colorimetric Adenosine Sensor

Five-hundred microliters of 5′-Ade_(Au) (extinction at 522 nm equals 2.2) and 500 μL of 3′-A₁₂Ade_(Au) (SEQ ID NO: 44) (extinction at 522 nm equals 2.2) were mixed in the presence of 300 mM NaCl, 25 mM Tris acetate buffer, pH 8.2, and 100 nM of the adenosine aptamer/extension (Adenosine Linker). The sample was warmed to 65° C. for one minute and then allowed to cool slowly to 4° C. The nanoparticles changed color from red to dark purple during this process. The sample was centrifuged and the precipitates were collected and then dispersed in 2000 μL of the same buffer (300 mM NaCl, 25 mM Tris acetate, pH 8.2). The suspension was used for detection of adenosine.

Example 2 Colorimetric Detection of Adenosine

One-hundred microliters of the sensor suspension from Example 1 was added to a small volume of concentrated adenosine solution. For example, 2 μL of 50 mM adenosine was added to give a final concentration of 1 mM. The color change was monitored with a UV-vis spectrometer or by the naked eye.

Example 3 Monitoring the Performance of the Adenosine Sensor

The color change of the sample from Example 2 was monitored by UV-vis extinction spectroscopy. FIG. 4 is a graph relating the extinction ratios provided at specific wavelengths from a sample during disaggregation. The dashed line in FIG. 4 shows the strong extinction peak at 522 nm exhibited by separated 13 nm nanoparticles, which provide a deep red color. As may be seen from the solid line in FIG. 4, upon aggregation, the 522 nm peak decreases in intensity and shifts to longer wavelength, while the extinction at 700 nm region increases, resulting in a red-to-blue color transition. Therefore a higher extinction ratio at 522 to 700 nm is associated with the red color of separated nanoparticles, while a low extinction ratio is associated with the blue color of aggregated nanoparticles. This extinction ratio was used to monitor the aggregation state of the particles.

Example 4 Selectivity and Sensitivity of the Adenosine Sensor

To a quarts UV-vis spectrophotometer cell (Hellma, Germany) was added 100 μL of the adenosine sensor system prepared in Example 1. A small volume (1-5 μL) of solutions including adenosine, uridine, cytidine or guanosine was added to the spectrophotometer cell to bring the analyte concentration to the desired level in the cell.

The dispersion kinetics for each cell was monitored as a function of time using a Hewlett-Packard 8453 spectrophotometer. FIG. 5A is a graph depicting the ratios of extinction at 522 and 700 nm plotted as a function of time. As may be seen from the plots, only adenosine gave significant increase in the extinction ratio as a function of time, while uridine, cytidine, and guanosine provided a color change consistent with the background. Therefore, the high selectivity of the sensor was confirmed.

FIG. 5B is a graph depicting the correlation between the observed extinction ratios for the color change of the sensor system and the concentration of the adenosine analyte after five minutes of aggregation. The exceptional linearity of the sensor system was evident from about 0.1 to about 1.5 mM.

FIG. 5C is a graph depicting the extinction ratios for multiple adenosine analyte concentrations over a 6 minute time period. The graph demonstrates the ability of the sensor system to effectively differentiate between different analyte concentrations within a few minutes. Thus, the ability of the sensor system to provide accurate quantitative information was established.

In addition to the instrumental method of FIG. 5B, the color developed by the sensor was conveniently observed visually. A color progression from blue to red was seen as the adenosine concentration increased from 0 to 2 mM. Uridine, cytidine, and guanos provided a color similar to the background.

Example 5 Preparation of a Colorimetric Potassium Ion Sensor

FIGS. 6A-6B represent an analyte sensor system that includes an aptamer that folds in the presence of K(I). FIG. 6A provides the sequences of the extension and aptamer portions of a linker and of the oligonucleotide functionalized particles. FIG. 6B depicts the aptamer folding in the presence of the K(I) analyte. To prepare the K(I) sensor system, 500 μL of 5′-K(I)_(Au) (extinction at 522 nm equals 2.2) and 500 μL of 3′-A₁₂K(I)_(Au) (SEQ ID NO: 44) (extinction at 522 nm equals 2.2) were mixed in the presence of 300 mM NaCl, 25 mM Tris acetate buffer, pH 8.2, and 100 nM of the potassium ion aptamer/extension (Potassium Linker). The sample was warmed to 65° C. for one minute and then allowed to cool slowly to 4° C. The nanoparticles changed color from red to dark purple during this process. The sample was centrifuged and the precipitates were collected and dispersed in 10 μL of the same buffer (300 mM NaCl, 25 mM Tris acetate, pH 8.2). The suspension was used for detection of K⁺.

Example 6 Colorimetric Detection of Potassium

Metal ion solutions of Li⁺, Na⁺, K⁺, Rb⁺, or Cs⁺ ions were made by dissolving LiCl, NaCl, KCl, RbCl or CsCl salt, respectively, in deionized water to obtain an ion concentration of 3 M. From these metal ion stock solutions were prepared solutions containing 25 mM of Tris acetate buffer, pH 8.2, and 300 mM of Li⁺, Na⁺, K⁺, Rb⁺, or Cs⁺ ions. To each of these five solutions was added 1 μL of the K(I) sensor system from Example 5 for each 99 μL of the metal ion containing solution. Therefore, each solution contained ˜300 mM of Li⁺, Na⁺, K⁺, Rb⁺, or Cs⁺ metal ions and an additional 3 mM of Na⁺ ions as background. Each sample was heated to 65° C. and then cooled slowly to 4° C. in 1 hour. The color change was monitored with a UV-vis spectrometer or by the naked eye. FIG. 6C depicts the extinction ratio of the potassium ion sensor system in the presence of Li⁺, Na⁺, K⁺, Rb⁺, or Cs⁺ ions, thus confirming the selectivity of the sensor system to K(I).

Example 7 Preparation of a Colorimetric Cocaine Sensor

FIGS. 7A-7B represent an analyte sensor system that includes an aptamer that folds in the presence of cocaine. FIG. 7A provides the sequences of the extension and aptamer portions of the linker and of the oligonucleotide functionalized particles. FIG. 7B depicts the aptamer folding in the presence of the cocaine analyte. To prepare the cocaine sensor system, 500 μL of 5′-CocAu (extinction at 522 nm equals 2.2) and 500 μL of 3′-A12CocAu (SEQ ID NO: 44) (extinction at 522 nm equals 2.2) were mixed in the presence of 300 mM NaCl, 25 mM Tris acetate buffer, pH 8.2, and 100 nM of the cocaine aptamer/extension (Cocaine Linker). The sample was warmed to 65° C. for one minute and then allowed to cool slowly to 4° C. The nanoparticles changed color from red to dark purple during this process. The sample was centrifuged and the precipitates collected. The collected precipitates were then dispersed in 2000 μL of another buffer (150 mM NaCl, 25 mM Tris acetate, pH 8.2. The suspension was used for detection of cocaine.

Example 8 Colorimetric Detection of Cocaine

One-hundred microliters of the above prepared cocaine sensor suspension were combined with a small volume of concentrated cocaine solution. For example, 1 μL of 100 mM cocaine was added to the suspension to give a final concentration of 1 mM. The color change was monitored with a UV-vis spectrometer or by the naked eye.

Example 9 Selectivity and Sensitivity of the Cocaine Sensor

To a quarts UV-vis spectrophotometer cell (Hellma, Germany) was added 100 μL of the cocaine sensor system prepared in Example 7. A small volume (0.5-2 μL) of solutions including cocaine, adenosine, or sucrose was added to the spectrophotometer cell to bring the analyte concentration to the desired level in the cell.

The dispersion kinetics for each cell was monitored as a function of time using a Hewlett-Packard 8453 spectrophotometer. FIG. 8A is a graph depicting the ratios of extinction at 522 and 700 nm plotted as a function of time. As may be seen from the plots, only cocaine gave a significant increase in the extinction ratio as a function of time, while adenosine and sucrose provided a color change consistent with the background. Therefore, the high selectivity of the sensor was confirmed.

FIG. 8B is a graph depicting the correlation between the observed extinction ratios for the color change of the sensor system and the concentration of the cocaine analyte after one minute of aggregation. The exceptional linearity of the sensor system was evident from about 0.1 to about 1 mM.

FIG. 8C is a graph depicting the extinction ratios for multiple cocaine analyte concentrations over a 5 minute time period. The graph demonstrates the ability of the sensor system to effectively differentiate between different analyte concentrations within a few minutes. Thus, the ability of the sensor system to provide accurate quantitative information was established.

In addition to the instrumental method of FIG. 8B, the color developed by the sensor was conveniently observed visually. A color progression from blue to red was seen as the cocaine concentration increased from 0 to 1 mM. Adenosine and sucrose provided a color similar to the background.

As any person of ordinary skill in the art will recognize from the provided description, figures, and examples, that modifications and changes can be made to the preferred embodiments of the invention without departing from the scope of the invention defined by the following claims and their equivalents. 

What is claimed is:
 1. A method of detecting an analyte, comprising: combining an aggregate with a sample; and detecting a color change responsive to the analyte in the sample, the aggregate comprising: a linker, wherein the linker is a single oligonucleotide comprising an aptamer that is capable of folding in response to the analyte; and first particles coupled to a first oligonucleotide, the first oligonucleotide complementary to at least a portion of the aptamer, wherein binding of the analyte to the aptamer causes disaggregation of the aggregate the disaggregated aggregate is detectable as a color change.
 2. A method for determining the sensitivity and selectivity of an aptamer to an analyte, comprising: combining an aggregate with the analyte; detecting a color change responsive to the analyte, the aggregate comprising: a linker, wherein the linker is a single oligonucleotide comprising the aptamer; and first particles coupled to a first oligonucleotide, the first oligonucleotide complementary to at least a portion of the aptamer, wherein binding of the analyte to the aptamer causes disaggregation of the aggregate and the disaggregated aggregate are detectable as a color change; and determining if the aptamer folded to provide the color change, thereby determining the sensitivity and selectivity of the aptamer.
 3. The method of claim 2, the aggregate further comprising second particles coupled to a second oligonucleotide, the second oligonucleotide complementary to at least a portion of an extension that forms a portion of the linker, wherein the extension comprises bases.
 4. The method of claim 3, where the extension comprises from 1 to 100 bases, at least 50% of the bases complementary to the first or second oligonucleotide.
 5. The method of claim 2, where the linker further comprises an extension.
 6. The method of claim 3, where at least a portion of the bases forming the extension inhibit the linker from forming an inherently stable secondary structure without the analyte.
 7. The method of claim 3, where a portion of the second oligonucleotide is not complementary to the extension.
 8. The method of claim 3, where the hybridization stability of the aptamer in combination with the analyte is greater than the hybridization stability of a portion of the aptamer with the first oligonucleotide.
 9. The method of claim 3, where the first and second particles comprise a material selected from the group consisting of metals, semiconductors, magnetizable materials, and combinations thereof.
 10. The method of claim 3, where the first and second particles comprise gold.
 11. The method of claim 2, where the analyte is a metal ion.
 12. The method of claim 2, where the analyte is selected from the group consisting of large biomolecules, small biomolecules, and organic molecules.
 13. The method of claim 2, where the linker oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NOS: 46, 52, and
 54. 14. The method of claim 2, where the linker oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NOS: 1-42.
 15. The method of claim 2 having a response time of less than 60 minutes.
 16. The method of claim 2 having a response time of less than 10 minutes at 23° to 37° C.
 17. The method of claim 1, wherein the first oligonucleotide is further complementary to at least a portion of an extension that forms a portion of the linker.
 18. The method of claim 1, the aggregate further comprising second particles coupled to a second oligonucleotide, the second oligonucleotide complementary to at least a portion of an extension that forms a portion of the linker.
 19. The method of claim 18, where the hybridization stability of the aptamer in combination with the analyte is greater than the hybridization stability of a portion of the aptamer with the second oligonucleotide.
 20. The method of claim 18, where the extension comprises from 1 to 100 bases, and at least 50% of the bases are complementary to the first or second oligonucleotide.
 21. The method of claim 1, where the linker further comprises an extension.
 22. The method of claim 18, where the first and second particles comprise a material selected from the group consisting of metals, semiconductors, magnetizable materials, and combinations thereof.
 23. The method of claim 1, where the analyte is a metal ion.
 24. The method of claim 1, where the analyte is selected from the group consisting of large biomolecules, small biomolecules, and organic molecules.
 25. The method of claim 1, where the linker oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NOS: 46, 52, and
 54. 26. The method of claim 1, where the linker oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NOS: 1-42.
 27. The method of claim 1, where the linker oligonucleotide comprises a variant of a sequence selected from the group consisting SEQ ID NOS: 1-42, 46, 52, 54, and wherein the variant has one or more bases of that portion of the sequence that hybridizes to the first oligonucleotide, and the corresponding bases on the first oligonucleotide are also modified to maintain hybridization pairings C-G and A-T.
 28. The method of claim 2, where the linker oligonucleotide comprises a variant of a sequence selected from the group consisting SEQ ID NOS: 1-42, 46, 52, 54, and wherein the variant has one or more bases of that portion of the sequence that hybridizes to the first oligonucleotide, and the corresponding bases on the first oligonucleotide are also modified to maintain hybridization pairings C-G and A-T.
 29. The method of claim 18, where the first and second particles comprise gold.
 30. A method of detecting an analyte, comprising: combining an aggregate with a sample; and detecting a color change responsive to the analyte in the sample, the aggregate comprising: a linker, wherein the linker is a single oligonucleotide comprising an extension and an aptamer that is capable of folding in response to the analyte; and first particles coupled to a first oligonucleotide, the first oligonucleotide complementary to at least a portion of the aptamer, second particles coupled to a second oligonucleotide, the second oligonucleotide complementary to at least a portion of the extension, wherein binding of the analyte to the aptamer causes disaggregation of the aggregate and the disaggregated aggregate is detectable as a color change. 